When arriving from Third Countries (non-EU countries, like the Russian Federation) the first stop should be preferably in ports listed as border checkpoints to contact officials and pass customs procedures shortly after mooring. For example, suitable destinations are Dirhami (north-west Estonia), Sillamäe (north-east), Praaga (Lake Peipsi), Roomassaare (Saaremaa Island, open 24 h). You must also report in to the officials at least one hour before leaving Estonia.
To clear customs, the list of crew members must be presented. Also keep in mind that it is not allowed to bring any meat or dairy products from Third Countries, and a limited amount of tobacco products, alcohol, and motor fuel are allowed. See more from Tax and Customs Board webpage.